Displaying 5 results from an estimated 5 matches for "groupinglist".
2011 May 12
1
Fw: Help with PLSR
...and 94,272
columns each representing a peptide.
>str(FullDataListTrans)
num [1:40, 1:94727] 42 40.9 65 56 61.7 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:40] "X" "X.1" "X.12" "X.13" ...
..$ : NULL
I have also created a vector "GroupingList" which gives the groupnames for each
respective sample(row).
> GroupingList
[1] 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4
[39] 4 4
> str(GroupingList)
int [1:40] 1 1 1 1 1 1 1 1 1 1 ...
I am now stuck while conducting the plsr. I have tried various...
2011 May 18
1
Help with Memory Problems (cannot allocate vector of size)
While doing pls I found the following problem
> BHPLS1 <- plsr(GroupingList ~ PCIList, ncomp = 10, data = PLSdata, jackknife =
>FALSE, validation = "LOO")
when not enabling jackknife the command works fine, but when trying to enable
jackknife i get the following error.
>BHPLS1 <- plsr(GroupingList ~ PCIList, ncomp = 10, data = PLSdata, jackknife =...
2011 May 17
1
Help with PLSR with jack knife
...am trying to identify the Biomarkers (i.e. most significant
peptides). I beleive that PLS with jack knifing, or alternativeley
CMV(cross-model-validation) are multivariateThe 40 samples belong to four
different groups.
I have managed to conduct the plsr using the commands:
BHPLS1 <- plsr(GroupingList ~ PCIList, ncomp = 10, data = PLSdata, validation =
"LOO")
and
BHPLS1 <- plsr(GroupingList ~ PCIList, ncomp = 10, data = PLSdata, validation =
"CV")
I have also used the following command to obtain the loadings
BHPLS1_Loadings <- loadings(BHPLS1)
Now I am unsure of...
2011 Nov 07
1
repeating a loop
...tsFeature)
BoxplotsData <- as.numeric(which(PCIList == BoxplotsFeature))
BoxplotsData <- TotalIntensityList[BoxplotsData,]
BoxplotsHeading <- paste("Tukey boxplot (including outliers) for PCI ", BoxplotsFeature , sep = "")
bplot(as.numeric(BoxplotsData), GroupingList, style = "tukey", outlier = TRUE,
col="red", main = BoxplotsHeading,
xlab = "Groups", ylab = "Normalised Intensity", plot = TRUE)
BoxplotsFilename <- paste(BoxplotsFeature, "_Boxplot", sep = "")
savePlot(filename = "...
2011 May 17
1
help with PLSR Loadings
...Named num [1:10] 14.57 6.62 7.59 5.91 3.26 ...
..- attr(*, "names")= chr [1:10] "Comp 1" "Comp 2" "Comp 3" "Comp 4" ...
Here is the structure of teh data used to conduct plsr
>str(PLSdata)
'data.frame': 40 obs. of 2 variables:
$ GroupingList: int 1 1 1 1 1 1 1 1 1 1 ...
$ PCIList : AsIs [1:40, 1:94727] 42.01749.... 40.85915.... 65.01948....
55.98204.... 61.71673.... ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr "X" "X.1" "X.12" "X.13" ...
.. ..$ : NULL
Because of thi...